On Mon, Sep 02, 2013, X Sun wrote:
>
> I am using Amber11 to do a similiar simulation of tuturial B1 with TIP3P
> water. In the first minimization, I fixed the protein and moved the
> water molecules, it's normal. In the second minimization, equilibrizing
> the whole system, this step aborted. I didn't have a clue why this
> happened. The input file is following,
You have to use shake when working with rigid water models like TIP3P.
> cut = 12.0
Use the default of 8.0 here (unless you are sure you know what you are doing).
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Received on Tue Sep 03 2013 - 05:00:02 PDT
